Variant report

Variant	rs559341
Chromosome Location	chr1:176144042-176144043
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:176116758..176118552-chr1:176143991..176146342,2	MCF-7	breast:
2	chr1:176141778..176145305-chr1:176175202..176178321,3	K562	blood:

Variant related genes	Relation type
ENSG00000236021	Chromatin interaction
ENSG00000143207	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10158829	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10494496	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs10737316	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10798431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10798433	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10798435	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10913150	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11804926	0.97[ASN][1000 genomes]
rs11806468	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11809136	1.00[CEU][hapmap];0.97[ASN][1000 genomes]
rs11809835	0.97[ASN][1000 genomes]
rs12239888	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16849522	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16849571	0.97[ASN][1000 genomes]
rs1831447	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2039231	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2039232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481627	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2481634	0.81[ASN][1000 genomes]
rs2481639	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481641	1.00[CHB][hapmap]
rs2481647	1.00[CHB][hapmap]
rs2481653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2481657	1.00[CHB][hapmap]
rs2481660	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2502822	1.00[CHB][hapmap]
rs2502824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2502825	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2502826	1.00[CHB][hapmap]
rs2502832	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2502834	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2502835	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2502836	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2502841	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2502842	1.00[CHB][hapmap]
rs2502847	0.81[ASN][1000 genomes]
rs3845368	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4543747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4650936	0.97[ASN][1000 genomes]
rs4652143	0.82[CHB][hapmap]
rs4652145	0.84[ASN][1000 genomes]
rs4652148	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4652150	0.90[ASN][1000 genomes]
rs4652151	0.97[ASN][1000 genomes]
rs4652152	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4652154	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4652155	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs471534	0.84[ASN][1000 genomes]
rs533403	0.81[ASN][1000 genomes]
rs553852	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs55969691	0.97[ASN][1000 genomes]
rs55979360	0.84[ASN][1000 genomes]
rs56367284	0.81[ASN][1000 genomes]
rs56981673	0.97[ASN][1000 genomes]
rs57395528	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57469471	0.85[ASN][1000 genomes]
rs580978	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs58178699	0.97[ASN][1000 genomes]
rs58305404	0.94[ASN][1000 genomes]
rs58325269	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58743849	0.97[ASN][1000 genomes]
rs59373738	0.97[ASN][1000 genomes]
rs598177	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs599326	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611883	0.81[ASN][1000 genomes]
rs61451700	0.97[ASN][1000 genomes]
rs61821029	0.81[ASN][1000 genomes]
rs6425370	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6672278	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6688211	1.00[CHB][hapmap]
rs6704509	1.00[CHB][hapmap]
rs704825	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704827	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs704830	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs704831	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73040925	0.84[ASN][1000 genomes]
rs73040940	0.97[ASN][1000 genomes]
rs73040951	0.97[ASN][1000 genomes]
rs73042718	0.97[ASN][1000 genomes]
rs73042723	0.97[ASN][1000 genomes]
rs73042728	0.85[ASN][1000 genomes]
rs73042741	0.97[ASN][1000 genomes]
rs73042749	0.97[ASN][1000 genomes]
rs74127189	0.81[ASN][1000 genomes]
rs74127190	0.97[ASN][1000 genomes]
rs7521561	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7536464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7539247	1.00[CHB][hapmap]
rs7543769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7553184	1.00[CHB][hapmap]
rs791800	0.81[ASN][1000 genomes]
rs796933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796934	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9783047	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv872565	chr1:176058782-176172795	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176065600-176154800	Weak transcription	Aorta	Aorta
2	chr1:176070400-176151400	Weak transcription	Pancreas	Pancrea
3	chr1:176100800-176153200	Weak transcription	Colonic Mucosa	Colon
4	chr1:176110600-176164000	Weak transcription	NHLF	lung
5	chr1:176116000-176146200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:176123800-176144200	Weak transcription	Left Ventricle	heart
7	chr1:176123800-176150000	Weak transcription	Osteobl	bone
8	chr1:176126400-176168800	Weak transcription	Small Intestine	intestine
9	chr1:176127000-176147000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:176127000-176174000	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:176127200-176153400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:176127400-176144200	Weak transcription	A549	lung
13	chr1:176127400-176153400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:176127400-176155400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:176128000-176144200	Weak transcription	Gastric	stomach
16	chr1:176128000-176147000	Weak transcription	Stomach Mucosa	stomach
17	chr1:176128000-176157800	Weak transcription	Spleen	Spleen
18	chr1:176128000-176175200	Weak transcription	Esophagus	oesophagus
19	chr1:176128400-176154600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:176128600-176147000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:176128600-176147200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:176128600-176155600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:176128800-176152800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:176128800-176152800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:176128800-176154200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:176132200-176154200	Weak transcription	NH-A	brain
27	chr1:176134400-176152800	Weak transcription	Brain Angular Gyrus	brain
28	chr1:176135200-176144600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:176136200-176147400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:176137400-176173000	Weak transcription	Right Ventricle	heart
31	chr1:176138200-176155800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:176138600-176146200	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr1:176138800-176144800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:176138800-176145400	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:176138800-176146000	Strong transcription	Liver	Liver
36	chr1:176138800-176146200	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr1:176138800-176155400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr1:176139000-176145400	Strong transcription	Fetal Thymus	thymus
39	chr1:176139000-176153800	Strong transcription	Dnd41	blood
40	chr1:176139200-176144600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:176139200-176146000	Strong transcription	Primary T cells from cord blood	blood
42	chr1:176139400-176144800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr1:176139400-176145000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:176139400-176146000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr1:176139600-176145200	Strong transcription	Adipose Nuclei	Adipose
46	chr1:176139800-176149200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:176139800-176152600	Weak transcription	Brain Anterior Caudate	brain
48	chr1:176140000-176145000	Weak transcription	Fetal Brain Male	brain
49	chr1:176140000-176155800	Weak transcription	Fetal Brain Female	brain
50	chr1:176140000-176157800	Weak transcription	H1 Cell Line	embryonic stem cell

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